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Fix species leakage with group-aware train/val split; val_loss kl_wei…
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Fix dead checkpoint_hub reference in .gitignore, point to real archive
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Fix stale src/losses/padic_geodesic.py references in CLAUDE.md
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Fase 3 result: taxonomy-conditioned held-out generalization also nega…
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Fase 2 of taxonomy-conditioned embedding plan: species-level holdout
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Fase 0-1 of taxonomy-conditioned embedding plan ("Condition D")
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Surface the cytochrome c negative result in CLAUDE.md itself
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Full runs + zero-model baseline: negative result for p-adic phylogeny…
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Document current status and exact next step in phylogeny validation plan
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Fix 10 findings from deep review of the Fase 4 evaluation script
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Graph Update: pip in /. #1464924183
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Phases 2-3 of phylogeny validation pipeline: alignment + 3 training c…
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Graph Update: pip in /. #1464149471
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Phase 1 of phylogeny validation pipeline: fetch cytochrome c + taxonomy
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Add phylogeny validation pipeline plan to docs/plans/
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Document dead StateNet fields; remove PRESETS_DIR pointing nowhere
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Finish maintainability pass on src/analysis/ and src/symbolic/
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Fix reversed digit order in seq_to_ternary_index; update stale script…
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Remove unused create_manifold_parameter/create_manifold_tensor
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Dedupe ternary_add/ternary_mul; remove dead EpochMetrics/ControllerState
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Graph Update: pip in /., /src/training #1461863778
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Dedupe inner_radius < outer_radius validator across 4 loss configs
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Graph Update: pip in /src/training #1461743093
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Remove dead hw_monitor threading, hoist all_params out of batch loop
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Codebase-wide dedup pass: losses, models/geometry/config, training/ut…
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